and of course you should know the meaning of each parameter, which you can find in the manual (posted by @themysticgeek)
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Optimized parameters for trimming single-end reads using Trimmomatic
Can anyone recommend a guide for choosing values for parameters when using Trimmomatic? I ran fastqc on the sequences after converting them to fastq format, and the results seemed to indicate the presence of adapter sequences. I am processing single-end reads (from a tomato seedling RNA-seq experiment, http://www.ncbi.nlm.nih.gov/sra/?term=SRR948460). I could not find a guide explaining in-depth what each parameter means, and I'm not sure how to decide besides trial and error (except I know to specify SE and -phred 33). Thank you!
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2 answers
I found the guide at http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.30.pdf
pretty detailed. It does explain all the parameters in sufficient detail.
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unfortunately there is no general rule for these parameters. the optimal values really depend on your data. what you can do is focusing on a small subset of the reads and check the presence of the adapters after choosing different values for the trimming parameters (using fastqc for example). in practice, you can make for-loops in bash, assigning different combinations of parameters values. then for each of the results you could check the fastqc output. finally you would choose the least "aggressive" parameters that allow an efficient removal of the adapters.
if you're also checking the quality of the reads, you can iterate also the quality-trimming parameters.
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